Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Purine nucleoside phosphorylase DeoD-type

Gene

deoD3

Organism
Vibrio fischeri (strain ATCC 700601 / ES114)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.UniRule annotation
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei5Purine nucleoside; shared with dimeric partnerBy similarity1
Binding sitei21Phosphate; via amide nitrogenBy similarity1
Binding sitei25PhosphateBy similarity1
Binding sitei44Phosphate; shared with dimeric partnerBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Names & Taxonomyi

Protein namesi
Recommended name:
Purine nucleoside phosphorylase DeoD-typeUniRule annotation (EC:2.4.2.1UniRule annotation)
Short name:
PNPUniRule annotation
Gene namesi
Name:deoD3UniRule annotation
Ordered Locus Names:VF_A0968
OrganismiVibrio fischeri (strain ATCC 700601 / ES114)
Taxonomic identifieri312309 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeAliivibrio
Proteomesi
  • UP000000537 Componenti: Chromosome II

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000631731 – 239Purine nucleoside phosphorylase DeoD-typeAdd BLAST239

Interactioni

Subunit structurei

Homohexamer.UniRule annotation

Protein-protein interaction databases

STRINGi312309.VF_A0968.

Structurei

Secondary structure

1239
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi15 – 19Combined sources5
Helixi23 – 33Combined sources11
Beta strandi35 – 41Combined sources7
Helixi43 – 45Combined sources3
Beta strandi48 – 53Combined sources6
Beta strandi56 – 61Combined sources6
Helixi67 – 78Combined sources12
Turni79 – 81Combined sources3
Beta strandi85 – 94Combined sources10
Beta strandi104 – 112Combined sources9
Helixi116 – 120Combined sources5
Turni121 – 123Combined sources3
Helixi132 – 143Combined sources12
Beta strandi149 – 156Combined sources8
Helixi166 – 173Combined sources8
Beta strandi178 – 182Combined sources5
Helixi183 – 193Combined sources11
Beta strandi196 – 206Combined sources11
Turni207 – 210Combined sources4
Helixi215 – 235Combined sources21

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LDNX-ray1.48A1-239[»]
ProteinModelPortaliQ5DYV8.
SMRiQ5DYV8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni88 – 91Phosphate bindingBy similarity4
Regioni180 – 182Purine nucleoside bindingBy similarity3
Regioni204 – 205Purine nucleoside bindingBy similarity2

Sequence similaritiesi

Belongs to the PNP/UDP phosphorylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0813. LUCA.
HOGENOMiHOG000274896.
KOiK03784.
OMAiFAMIADF.
OrthoDBiPOG091H021M.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
HAMAPiMF_01627. Pur_nucleosid_phosp. 1 hit.
InterProiIPR004402. DeoD-type.
IPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
IPR000845. Nucleoside_phosphorylase_d.
[Graphical view]
PANTHERiPTHR21234. PTHR21234. 1 hit.
PfamiPF01048. PNP_UDP_1. 1 hit.
[Graphical view]
SUPFAMiSSF53167. SSF53167. 1 hit.
TIGRFAMsiTIGR00107. deoD. 1 hit.
PROSITEiPS01232. PNP_UDP_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5DYV8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTPHINAPL DAFADTILMP GDPLRAKLIA ETYLENVVQV TDVRGMLGFT
60 70 80 90 100
GEFKGRKISV MGHGMGAPSA SIYFHELMTT YKVKNFIRIG SCGAIHDDVK
110 120 130 140 150
LKDLIVAIGA STDSKMNRIR FKDNDFAATA NYNMLSECVN TLKTTDINYL
160 170 180 190 200
VGNVFSSDLF YRPDEEQYDM MARYGILGVE MEVNALYSAA AENHCNAVAL
210 220 230
CTVTDHIKNH EHLTADERRT ELHEMINVAL DVALKLPTE
Length:239
Mass (Da):26,542
Last modified:March 15, 2005 - v1
Checksum:i0B35489AA6A19951
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000021 Genomic DNA. Translation: AAW88038.1.
RefSeqiWP_005423543.1. NC_006841.2.
YP_206926.1. NC_006841.2.

Genome annotation databases

EnsemblBacteriaiAAW88038; AAW88038; VF_A0968.
GeneIDi3280781.
KEGGivfi:VF_A0968.
PATRICi20117931. VBIVibFis127983_3569.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000021 Genomic DNA. Translation: AAW88038.1.
RefSeqiWP_005423543.1. NC_006841.2.
YP_206926.1. NC_006841.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LDNX-ray1.48A1-239[»]
ProteinModelPortaliQ5DYV8.
SMRiQ5DYV8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi312309.VF_A0968.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAW88038; AAW88038; VF_A0968.
GeneIDi3280781.
KEGGivfi:VF_A0968.
PATRICi20117931. VBIVibFis127983_3569.

Phylogenomic databases

eggNOGiCOG0813. LUCA.
HOGENOMiHOG000274896.
KOiK03784.
OMAiFAMIADF.
OrthoDBiPOG091H021M.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
HAMAPiMF_01627. Pur_nucleosid_phosp. 1 hit.
InterProiIPR004402. DeoD-type.
IPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
IPR000845. Nucleoside_phosphorylase_d.
[Graphical view]
PANTHERiPTHR21234. PTHR21234. 1 hit.
PfamiPF01048. PNP_UDP_1. 1 hit.
[Graphical view]
SUPFAMiSSF53167. SSF53167. 1 hit.
TIGRFAMsiTIGR00107. deoD. 1 hit.
PROSITEiPS01232. PNP_UDP_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDEOD3_VIBF1
AccessioniPrimary (citable) accession number: Q5DYV8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: March 15, 2005
Last modified: November 2, 2016
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.